Genome assembly of the Canadian two-row malting barley cultivar AAC Synergy

Citation

Wayne Xu, James R Tucker, Wubishet A Bekele, Frank M You, Yong-Bi Fu, Raja Khanal, Zhen Yao, Jaswinder Singh, Brian Boyle, Aaron D Beattie, François Belzile, Martin Mascher, Nicholas A Tinker, Ana Badea, Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy, G3 Genes|Genomes|Genetics, 2021;, jkab031, https://doi.org/10.1093/g3journal/jkab031

Plain language summary

Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row (which means all the spikelets are fertile) barley cv. Morex reference genome (which is a nucleic acid sequence database assembled as a representative example of the set of genes in one individual organism) has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic analyses when working in two-row (which means that only the central spikelet is fertile) germplasm that is more common to Canadian malting barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cv. AAC Synergy. The completeness and annotation (which is the process of identifying the locations of genes) of the assembly were assessed by comparing it with the updated version of Morex (six-row) and the recently released Golden Promise (two-row) genome assemblies.

Abstract

Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cv. Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian malting barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cv. AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, an N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with current Morex and Golden Promise genome assemblies.